Difference between revisions of "Team:HebrewU/Plant"

(Prototype team page)
 
 
(18 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
{{HebrewU}}
+
<html lang="en">
−
<html>
+
<head>
 +
<title>HebrewU HujiGEM 2018</title>
 +
<meta charset="utf-8">
 +
<meta name="viewport" content="width=device-width, initial-scale=1">
  
 +
<!--- Own CSS --->
 +
<link rel="stylesheet" href="https://2018.igem.org/Template:HebrewU/CSS?action=raw&ctype=text/css">
  
−
<div class="column full_size judges-will-not-evaluate">
+
<!--- Main Menu script --->
−
<h3>★  ALERT! </h3>
+
<script type="text/javascript" src="https://2018.igem.org/Template:Hebrewu/Javascript?action=raw&ctype=text/javascript"></script>
−
<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
+
−
<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
+
−
</div>
+
  
 +
<!--- w3 Css --->
 +
<link rel="stylesheet" href="https://2018.igem.org/Template:HebrewU/w3?action=raw&ctype=text/css">
  
−
<div class="clear"></div>
+
<!--- Bootstrap Css --->
 +
  <script src="https://2018.igem.org/Template:HebrewU/boot?action=raw&ctype=text/javascript"></script>
 +
  <link rel="stylesheet" href="https://2018.igem.org/Template:HebrewU/strap?action=raw&ctype=text/css">
 +
 
 +
  <!--- Open interview in new window --->
 +
<script type="text/javascript">
 +
            function openTab(th)
 +
            {
 +
                window.open(th.name,'_blank');
 +
            }
 +
</script>
 +
       
 +
       
 +
<style>
 +
/* Disable I-GEM defult properties for blank page */
 +
    #sideMenu, #top_title {display:none;}
 +
    #sideMenu, #sideMenu *, #top_menu_inside, #top_menu_inside *{box-sizing: initial; -webkit-box-sizing: initial;}
 +
    #content { padding:0px; width:100%; margin-top:-12px; margin-left:0px;}
 +
    #body {background-color:#EDEADC; }
 +
    #bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 { margin-bottom: 0px; }
 +
 +
    .w3-container {
 +
  overflow: auto;
 +
    }
 +
 +
* {
 +
  -webkit-box-sizing:content-box ;
 +
    -moz-box-sizing:content-box ;
 +
    box-sizing:content-box ;
 +
    }
  
  
−
<div class="column full_size">
+
.ahuji {
−
<h1> Plant Synthetic Biology</h1>
+
    color:black
 +
    }
 +
 
 +
 
 +
 
 +
@media (max-width: 1000px) {
 +
    .fixed {
 +
    display: none;
 +
    }
 +
 
 +
.ulogo { display:none; }
 +
}
 +
 
 +
#panel, #flip_experts #panel_industry {
 +
    padding: 5px;
 +
    text-align: center;
 +
}
 +
 
 +
#panel panel_industry{
 +
    padding: 50px;
 +
    display: none;
 +
}
 +
 
 +
body {
 +
background-color:w3-blue-gray;
 +
 +
}
 +
 
 +
ul {
 +
 +
padding-left:150px;
 +
padding-right:100px;
 +
 
 +
 +
}
 +
 
 +
 
 +
#HQ_page p {
 +
    font-family: Tahoma, Geneva, sans-serif;
 +
    font-size:20px;
 +
    color: white;
 +
}
 +
 
 +
a {
 +
color:yellow;
 +
 +
}
 +
 
 +
a:visited {
 +
color:yellow;
 +
}
 +
 
 +
a:hover{
 +
color:yellow;
 +
 +
}
 +
 
 +
</style>
 +
 
 +
<script>
 +
function myFunction() {
 +
    var x = document.getElementById("Industry_display");
 +
    if (x.className.indexOf("w3-show") == -1) {
 +
        x.className += " w3-show";
 +
    } else {
 +
        x.className = x.className.replace(" w3-show", "");
 +
    }
 +
}
 +
</script>
 +
 
 +
<script>
 +
function myFunction_2() {
 +
    var x = document.getElementById("Interviews_display");
 +
    if (x.className.indexOf("w3-show") == -1) {
 +
        x.className += " w3-show";
 +
    } else {
 +
        x.className = x.className.replace(" w3-show", "");
 +
    }
 +
}
 +
</script>
 +
 
 +
<body>
 +
<div class="w3-blue-gray">
 +
<ul id="ddmenu_hebrewu">
 +
            <li style="float:left;margin-top:12px;padding-left:15px;"><br />Hebrew</li>
 +
 
 +
    <div class="huji_homebutton">
 +
           
 +
        <a href="javascript:void(0);" class="icon" onClick="show_small_nav()">
 +
            <img src="https://static.igem.org/mediawiki/2018/d/dc/T--Hebrewu--huji_small_manu.png" width="20" height="20" padding:"2px">
 +
        </a>
 +
   
 +
        <a href="https://2018.igem.org/Team:HebrewU">
 +
                <img class="ulogo" src="https://static.igem.org/mediawiki/2018/d/d3/T--Hebrewu--huji_boiling_logo.png" width="60" height="60" style="margin-left:-27px;">
 +
                </a>
 +
  </div>
 +
 
 +
    <li><a>Project</a>
 +
        <ul>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Description">Description</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Model">Model</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Demonstrate">Results</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Parts">Parts</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Software">MOOLTi</a></li>
 +
 
 +
        </ul>       
 +
    </li>
 +
    <li><a>Lab</a>
 +
        <ul>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Design">Yeast Design</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Plant">Plant Design</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Notebook">Notebook</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/InterLab">Inter-lab</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Safety">Safety</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Protocols">Protocols</a></li>
 +
        </ul>
 +
       
 +
    </li>
 +
 
 +
   
 +
    <li><a href="https://2018.igem.org/Team:HebrewU/Human_Practices">Human Practices</a>
 +
        <ul>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Ethics">Ethics</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Global_aspects">Global Aspects</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Public_engagment">Public Engagment</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Open_Source">Open Source</a></li>
 +
        </ul>
 +
    </li>
 +
   
 +
    <li><a>Team</a>
 +
        <ul>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Team">Members</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Attributions">Attributions</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Collaborations">Collaborations</a></li>
 +
            <li><a href="https://2018.igem.org/Team:HebrewU/Photo_Gallery">Photo Gallery</a></li>
 +
        </ul>
 +
    </li>
 +
            <li ><a href="https://2018.igem.org/Team:HebrewU/Judging">Judging</a></li>
 +
           
 +
    <div class="social_huji">
 +
            <a href="https://twitter.com/GemHuji"> <img class="social_icons" src="https://static.igem.org/mediawiki/2018/3/39/T--Hebrewu--twitter_logo.png" width="25" height="25"></a>
 +
            <a href="https://www.facebook.com/HUJiGEM"> <img class="social_icons" src="https://static.igem.org/mediawiki/2018/8/8a/T--Hebrewu--facebook_logo.png" width="25" height="25"></a>
 +
            <a href="https://www.instagram.com/hujigem/"> <img class="social_icons" src="https://static.igem.org/mediawiki/2018/5/54/T--Hebrewu--insta_logo.png" width="25" height="25"></a>
 +
            <a href="https://www.igem.org/Main_Page"> <img class="social_icons" src="https://static.igem.org/mediawiki/2018/1/1a/T--Hebrewu--IGEM_logo.png" width="30"></a>
 +
 
 +
    </div> 
 +
 
 +
</ul>
 +
 
 +
<!----------- Responsive Navbar --------------->   
 +
<div class="huji_smallnav" id="huji_shownav">
 +
    <button class="huji_small_navbar">Project</button>
 +
        <div class="huji_small_navbar_panel">
 +
            <a href="https://2018.igem.org/Team:HebrewU/Description"><button class="b_huji_small_subnav">Description</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Model"><button class="b_huji_small_subnav">Model</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Demonstrate"><button class="b_huji_small_subnav">Results</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Parts"><button class="b_huji_small_subnav">Parts</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Software"><button class="b_huji_small_subnav">MOOLTi</button></a>
 +
        </div>
 +
 
 +
    <button class="huji_small_navbar">Lab</button>
 +
        <div class="huji_small_navbar_panel">
 +
            <a href="https://2018.igem.org/Team:HebrewU/Design"><button class="b_huji_small_subnav">Yeast Design</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Plant"><button class="b_huji_small_subnav">Plant Design</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Notebook"><button class="b_huji_small_subnav">Notebook</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/InterLab"><button class="b_huji_small_subnav">InterLab</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Safety"><button class="b_huji_small_subnav">Safety</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Protocols"><button class="b_huji_small_subnav">Protocols</button></a>
 +
 
 +
        </div>
 +
 
 +
    <button class="huji_small_navbar">Human Practice</button>
 +
        <div class="huji_small_navbar_panel">
 +
            <a href="https://2018.igem.org/Team:HebrewU/Human_Practices"><button class="b_huji_small_subnav">Human Practice - Main Page</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Ethics"><button class="b_huji_small_subnav">Ethics</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Global_aspects"><button class="b_huji_small_subnav">Global Aspects</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Public_Engagment"><button class="b_huji_small_subnav">Public Engagment</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Open_Source"><button class="b_huji_small_subnav">Open Source</button></a>
 +
        </div>
 +
 
 +
 
 +
     
 +
          <button class="huji_small_navbar">Team</button>
 +
        <div class="huji_small_navbar_panel">
 +
            <a href="https://2018.igem.org/Team:HebrewU/Members"><button class="b_huji_small_subnav">Members</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Attributions"><button class="b_huji_small_subnav">Attributions</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Collaborations"><button class="b_huji_small_subnav">Collaborations</button></a>
 +
            <a href="https://2018.igem.org/Team:HebrewU/Photo_Gallery"><button class="b_huji_small_subnav">Photo Gallery</button></a>
 +
        </div>
 +
       
 +
            <a href="https://2018.igem.org/Team:HebrewU/Judging"><button class="huji_small_navbar">Judging</button></a>
 
</div>
 
</div>
−
<div class="column two_thirds_size">
+
<!----------- Script 1 for small navbar --------------->
−
<h3>Best Advancement in Plant Synthetic Biology Special Prize</h3>
+
<script>
−
<p>iGEM introduced an award for plant synthetic biology for the first time in 2016. Many teams have worked in this area over the years, and we finally decided it was time for a special award to encourage teams in this area. Teams can work with a number of different plant and algal chassis to be eligible for this award. The prize will go to the team with the best plant synthetic biology project. As with all awards, if there are a sufficiently high number of participating teams, there will be separate awards for the undergraduate and overgraduate sections.  
+
        function show_small_nav() {
−
</p>
+
              var x = document.getElementById("huji_shownav");
 +
            if (x.style.display === "none") {
 +
                x.style.display = "block";
 +
            } else {
 +
                x.style.display = "none";
 +
            }
 +
        }
 +
    </script>
  
−
<p>
+
<!------------ Script 2 for small navbar ------------->
−
While not mandatory, teams are strongly encouraged to work with Phytobricks during your project.  
+
<script>
−
</p>
+
    var acc = document.getElementsByClassName("huji_small_navbar");
 +
    var i;
 +
   
 +
    for (i = 0; i < acc.length; i++) {
 +
        acc[i].addEventListener("click", function() {
 +
            this.classList.toggle("active");
 +
            var huji_small_navbar_panel = this.nextElementSibling;
 +
            if (huji_small_navbar_panel.style.display === "block") {
 +
                huji_small_navbar_panel.style.display = "none";
 +
            } else {
 +
                huji_small_navbar_panel.style.display = "block";
 +
            }
 +
        });
 +
    }
 +
    </script>
 +
    <a onClick="topFunction()" id="myBtn_up" title="Go to top"><img src="https://static.igem.org/mediawiki/2018/1/1e/T--hebrewu--arrow_up.png" width="40px" /></a>
  
−
<p>
 
−
Please put all your judging information relevant to the plants prize on this page!
 
  
 +
<script>
 +
// When the user scrolls down 20px from the top of the document, show the button
 +
window.onscroll = function() {scrollFunction()};
  
−
<br><br>
+
function scrollFunction() {
−
To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Advancement in Plant Synthetic Biology prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>.
+
    if (document.body.scrollTop > 20 || document.documentElement.scrollTop > 20) {
−
<br><br>
+
        document.getElementById("myBtn_up").style.display = "block";
−
You must also delete the message box on the top of this page to be eligible for this prize.
+
    } else {
−
</p>
+
        document.getElementById("myBtn_up").style.display = "none";
 +
    }
 +
}
  
−
</p>
+
// When the user clicks on the button, scroll to the top of the document
−
</div>
+
function topFunction() {
−
<div class="column third_size">
+
    document.body.scrollTop = 0;
−
<div class="highlight decoration_A_full">
+
    document.documentElement.scrollTop = 0;
−
<h3> Inspiration </h3>
+
}
−
<p>
+
</script>
−
Here are a few examples from previous teams:
+
<!------------ HP start ------------->
−
</p>
+
 
−
<ul>
+
<br /> <br />
−
<li><a href="https://2016.igem.org/Team:Cambridge-JIC">2016 Cambridge JIC</a></li>
+
 
−
<li><a href="https://2016.igem.org/Team:SCAU-China">2016 SCAU-China</a></li>
+
<!-- First Grid -->
−
</ul>
+
  <div class="blue-gray">
 +
<div class="w3-center w3-animate-zoom">
 +
            <img src="https://static.igem.org/mediawiki/2018/b/b0/T--hebrewu--Plant_Des_HL.png" width="35%">
 +
          <br />  
 +
        <br />  
 
</div>
 
</div>
 +
        <div class="content">
 +
        <p style="padding-left:150px;padding-right:150px;text-align:justify;line-height:1.5">
 +
        Our team's pathway was designed for plants. Despite analyzing the pathway in yeast, we always saw plants as our final frontier. On the <a href="https://2018.igem.org/Team:HebrewU/Open_Source">open source page</a>, we discuss plants such as pumpkins and wheat that are ideal for real-world application of our project, as well as mechanisms for sterilizing GMO plants. Sterilizing plants ensures that cross-pollination between GMOs and natural fauna cannot happen- allowing for the responsible implementation of our project. Working with the plants native features, utilizing roots for uptake and native enzymes we created a synergy between natural and synthetic biology. The engineered pathway ends with a product (pyrocatechol) which seamlessly enters plants metabolism via Polyphenol Oxidase enzymes, found in almost all plants. <sup>1</sup>
 +
 +
    </p> <br /> <br /> 
 +
    <div class="content">
 +
        <p style="padding-left:150px;padding-right:150px;text-align:justify;line-height:1.5">
 +
      The initial technologies for engineering the agrobacterium involved complex microbial genetic methodologies that inserted the gene of interest into the transfer DNA (T-DNA) region of the Ti-plasmids. However, as these technologies developed, and more research was done, biologists realized that the T-DNA genes did not have to sit on the same plasmid as the Vir (virulence) genes to successfully introduce genes into plants. Thus, the Binary Vector method was created, and this one big and complicated vector was split in two, easy to work with vectors. This binary system permitted simple manipulation of Agrobacterium and opened up the field of plant genetic engineering. It is composed of the borders of T-DNA, multiple cloning sites, replication functions for E. coli and A. tumefaciens, selectable marker genes, reporter genes, and other accessory elements that can improve the efficiency of and give the further capability to the system.<sup>2,3,4</sup>
 +
<br /><br />
 +
       
 +
       
 +
        <div class="w3-center">
 +
            <img src="https://static.igem.org/mediawiki/2018/e/e2/T--hebrewu--Plant_Des1.png" width="35%">
 +
          <br />
 +
        <br />
 +
</div>
 +
        <p style="padding-left:150px;padding-right:150px;text-align:justify;line-height:1.5">
 +
        We used the pHGHPB vector which contains all of the above mentioned features. In this vector, GFP and the inserted gene are fused by a Poly-A Bridge, creating a hybrid protein. Using this method, its ensured, that were ever we see GFP expression, we know that our protein is be expressed as well. In addition, Basta antibiotic resistance gene is expressed, allowing for easier identification of transgenic plants when grown on appropriate media. Both of these genes are regulated by the 35S promoter, derived from cauliflower mosaic virus, which is a constitutive promoter, active in all tissues of the plant.
 +
<br />  <br /> 
 +
We cloned multiple vectors with our genes, but only transformed plants with <a onClick="openTab(this)"  name="https://static.igem.org/mediawiki/2018/a/a5/T--Hebrewu--Dehalo_exper_fasta.txt">Haloacid Dehalogenase</a>. As each generation of Arabidopsis takes approximately 3 months to grow + transform, it was not possible to transform a plant with our entire pathway in the time we had for this year's competition. As such we decided to use the Dehalogenase, even though it does not completely breakdown the molecule, it partially dechlorinates TCDD, reducing its toxicity greatly. <br />  <br />   
 +
        </p>
 +
       
 +
        <div class="w3-center">
 +
            <img src="https://static.igem.org/mediawiki/2018/3/38/T--hebrewu--Plant_Des2.png" width="35%">
 +
          <br />
 +
        <br />
 +
</div>
 +
       
 +
       
 +
        <h2 style="padding-left:150px;padding-right:150px;text-align:justify;line-height:1.5"> References: </h2>
 +
        <p style="padding-left:150px;padding-right:150px;text-align:justify;line-height:1.5">
 +
           
 +
                1. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4294140/">"Beyond brown: polyphenol oxidases as enzymes of plant specialized metabolism"; M. Sullivan,Front Plant Sci. 2014; 5: 783.</a><br />
 +
             
 +
               
 +
                2. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2245830/">"T-DNA Binary Vectors and Systems"; L.Y. Lee,Plant, Physiol. 2008 Feb; 146(2): 325–332</a><br />
 +
               
 +
            3. <a href="https://link.springer.com/protocol/10.1385%2F1-59745-130-4%3A15#citeas">"Binary Vectors and Super-binary Vectors";T. Komari et. al, Humana Press-https://doi.org/10.1385/1-59745-130-4:15</a><br />
 +
           
 +
              4. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4292801/citedby/">"The Agrobacterium Ti Plasmids"; PJ Christie et. al,Microbiol Spectr. 2014; 2(6): 10.1128/microbiolspec.PLAS-0010-2013.</a><br />
 +
        </p><br /><br />
 +
       
 +
        </div>
 +
        </div>
 +
   
 +
   
 +
  </div>
 
</div>
 
</div>
  
−
<div class="clear"></div>
+
 
 +
</body>
 
</html>
 
</html>

Latest revision as of 17:30, 12 December 2018

HebrewU HujiGEM 2018





Our team's pathway was designed for plants. Despite analyzing the pathway in yeast, we always saw plants as our final frontier. On the open source page, we discuss plants such as pumpkins and wheat that are ideal for real-world application of our project, as well as mechanisms for sterilizing GMO plants. Sterilizing plants ensures that cross-pollination between GMOs and natural fauna cannot happen- allowing for the responsible implementation of our project. Working with the plants native features, utilizing roots for uptake and native enzymes we created a synergy between natural and synthetic biology. The engineered pathway ends with a product (pyrocatechol) which seamlessly enters plants metabolism via Polyphenol Oxidase enzymes, found in almost all plants. 1



The initial technologies for engineering the agrobacterium involved complex microbial genetic methodologies that inserted the gene of interest into the transfer DNA (T-DNA) region of the Ti-plasmids. However, as these technologies developed, and more research was done, biologists realized that the T-DNA genes did not have to sit on the same plasmid as the Vir (virulence) genes to successfully introduce genes into plants. Thus, the Binary Vector method was created, and this one big and complicated vector was split in two, easy to work with vectors. This binary system permitted simple manipulation of Agrobacterium and opened up the field of plant genetic engineering. It is composed of the borders of T-DNA, multiple cloning sites, replication functions for E. coli and A. tumefaciens, selectable marker genes, reporter genes, and other accessory elements that can improve the efficiency of and give the further capability to the system.2,3,4



We used the pHGHPB vector which contains all of the above mentioned features. In this vector, GFP and the inserted gene are fused by a Poly-A Bridge, creating a hybrid protein. Using this method, its ensured, that were ever we see GFP expression, we know that our protein is be expressed as well. In addition, Basta antibiotic resistance gene is expressed, allowing for easier identification of transgenic plants when grown on appropriate media. Both of these genes are regulated by the 35S promoter, derived from cauliflower mosaic virus, which is a constitutive promoter, active in all tissues of the plant.

We cloned multiple vectors with our genes, but only transformed plants with Haloacid Dehalogenase. As each generation of Arabidopsis takes approximately 3 months to grow + transform, it was not possible to transform a plant with our entire pathway in the time we had for this year's competition. As such we decided to use the Dehalogenase, even though it does not completely breakdown the molecule, it partially dechlorinates TCDD, reducing its toxicity greatly.



References:

1. "Beyond brown: polyphenol oxidases as enzymes of plant specialized metabolism"; M. Sullivan,Front Plant Sci. 2014; 5: 783.
2. "T-DNA Binary Vectors and Systems"; L.Y. Lee,Plant, Physiol. 2008 Feb; 146(2): 325–332
3. "Binary Vectors and Super-binary Vectors";T. Komari et. al, Humana Press-https://doi.org/10.1385/1-59745-130-4:15
4. "The Agrobacterium Ti Plasmids"; PJ Christie et. al,Microbiol Spectr. 2014; 2(6): 10.1128/microbiolspec.PLAS-0010-2013.